https://github.com/avinal/rstats-test
Binary Segmentation Project tests
https://github.com/avinal/rstats-test
Last synced: over 1 year ago
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Binary Segmentation Project tests
- Host: GitHub
- URL: https://github.com/avinal/rstats-test
- Owner: avinal
- License: mit
- Created: 2020-12-26T10:24:49.000Z (over 5 years ago)
- Default Branch: main
- Last Pushed: 2020-12-26T14:05:23.000Z (over 5 years ago)
- Last Synced: 2025-02-22T01:32:06.705Z (over 1 year ago)
- Language: R
- Size: 207 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# rstats-test
Binary Segmentation Project tests
## Easy
- Download data(*neuroblastoma*, package=”neuroblastoma”) and **plot profile.id=4**, **chromosome=2**, (**y=logratio**, ***x=position***).
```txt
total data points = 234
```
- Use *binsegRcpp* to compute binary segmentation models up to 5 segments (change in mean, normal distribution), then plot those segment means and changepoints on top of the data.
| S No. | 1 | 2 | 3 | 4 | 5 | 6 |
| --- | --- | --- | --- | --- | --- | --- |
| Segment | 1-41 | 42-113 | 114-146 | 147-152 | 153-157 | 158-234 |
| Mean | 0.351231083 | 0.005885206 | -0.447813047 | -0.307411681 | -0.666259257 | 0.003035709 |
| Changepoint | 41 | 113 | 146 | 152 | 157 | - |
## Medium
- Use the *changepoint* package to compute models up to 5 segments for the same data set.
| S No. | 1 | 2 | 3 | 4 | 5 | 6 |
| --- | --- | --- | --- | --- | --- | --- |
| Segment | 1-41 | 42-113 | 114-152 | 153-157 | 158-220 | 220-234 |
| Mean | 0.351231083 | 0.005885206 | -0.426212837 | -0.666259257 | 0.016075375 | -0.055642790
| Changepoint | 41 | 113 | 152 | 157 | 220 | - |
- Are the changepoints the same?
While most of the changepoints are same there are few variation, shown in table and in figure as blue box.
Package
Changepoints
binsegRcpp
41
113
146
152
157
changepoint
41
113
152
157
220
## Hard 1
- Implement Negative Binomial loss function in C code using the same arguments as in [changepoint/src/cost_general_functions.c]("https://github.com/rkillick/changepoint/blob/master/src/cost_general_functions.c").
## Hard 2
- Fork binsegRcpp and modify [src/binseg_normal.cpp]("https://github.com/tdhock/binsegRcpp/blob/master/src/binseg_normal.cpp") so that it computes change in mean and variance (instead of change of mean with constant variance).
- Use it to compute changepoints for the same neuroblastoma data set, and verify that the result is the same as the result of `changepoint::cpt.meanvar`.